This work was supported by the National Institutes of Health (P30GM103486).

<ol>
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B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alpaca+(Lama+pacos)+as+a+convenient+source+of+recombinant+camelid+heavy+chain+antibodies+(VHHs).">Alpaca (Lama pacos) as a convenient source of recombinant camelid heavy chain antibodies (VHHs).</a> Journal of Immunological Methods. 324 (1-2), 13-25 (2007).</li><li>Pardon, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+general+protocol+for+the+generation+of+Nanobodies+for+structural+biology.">A general protocol for the generation of Nanobodies for structural biology.</a> Nature Protocols. 9 (3), 674-693 (2014).</li><li>Hertveldt, K., Belien, T., Volckaert, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=General+M13+phage+display:+M13+phage+display+in+identification+and+characterization+of+protein-protein+interactions.">General M13 phage display: M13 phage display in identification and characterization of protein-protein interactions.</a> Methods in Molecular Biology. 502, 321-339 (2009).</li><li>Kushwaha, R., Schafermeyer, K. R., Downie, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+protocol+for+phage+display+and+affinity+selection+using+recombinant+protein+baits.">A protocol for phage display and affinity selection using recombinant protein baits.</a> Journal of Visualized Experiments. (84), e50685 (2014).</li><li>Hamers-Casterman, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Naturally+occurring+antibodies+devoid+of+light+chains.">Naturally occurring antibodies devoid of light chains.</a> Nature. 363 (6428), 446-448 (1993).</li><li>Muyldermans, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Camelid+immunoglobulins+and+nanobody+technology.">Camelid immunoglobulins and nanobody technology.</a> Veterinary Immunology and Immunopathology. 128 (1-3), 178-183 (2009).</li><li>Muyldermans, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanobodies:+natural+single-domain+antibodies.">Nanobodies: natural single-domain antibodies.</a> Annu Rev Biochem. 82, 775-797 (2013).</li><li>Muyldermans, S., Cambillau, C., Wyns, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recognition+of+antigens+by+single-domain+antibody+fragments:+the+superfluous+luxury+of+paired+domains.">Recognition of antigens by single-domain antibody fragments: the superfluous luxury of paired domains.</a> Trends in Biochemical Sciences. 26 (4), 230-235 (2001).</li><li>Wang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanobody-derived+nanobiotechnology+tool+kits+for+diverse+biomedical+and+biotechnology+applications.">Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications.</a> International Journal of Nanomedicine. 11, 3287-3303 (2016).</li><li>Van Saun, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nutritional+requirements+and+assessing+nutritional+status+in+camelids.">Nutritional requirements and assessing nutritional status in camelids.</a> Veterinary Clinics of North America: Food Animal Practice. 25 (2), 265-279 (2009).</li><li>Jones, M., Boileau, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Camelid+herd+health.">Camelid herd health.</a> Veterinary Clinics of North America: Food Animal Practice. 25 (2), 239-263 (2009).</li><li>Daley, L. P., Gagliardo, L. F., Duffy, M. S., Smith, M. C., Appleton, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Application+of+monoclonal+antibodies+in+functional+and+comparative+investigations+of+heavy-chain+immunoglobulins+in+new+world+camelids.">Application of monoclonal antibodies in functional and comparative investigations of heavy-chain immunoglobulins in new world camelids.</a> Clinical and Diagnostic Laboratory Immunology. 12 (3), 380-386 (2005).</li><li>Romao, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+Useful+Nanobodies+by+Phage+Display+of+Immune+Single+Domain+Libraries+Derived+from+Camelid+Heavy+Chain+Antibodies.">Identification of Useful Nanobodies by Phage Display of Immune Single Domain Libraries Derived from Camelid Heavy Chain Antibodies.</a> Current Pharmaceutical Design. 22 (43), 6500-6518 (2016).</li><li>Henry, K. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+TGF-beta-neutralizing+single-domain+antibodies+of+predetermined+epitope+specificity+using+next-generation+DNA+sequencing.">Isolation of TGF-beta-neutralizing single-domain antibodies of predetermined epitope specificity using next-generation DNA sequencing.</a> Protein Engineering, Design and Selection. 29 (10), 439-443 (2016).</li><li>Burg, J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+biology.+Structural+basis+for+chemokine+recognition+and+activation+of+a+viral+G+protein-coupled+receptor.">Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.</a> Science. 347 (6226), 1113-1117 (2015).</li><li>Wesolowski, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+domain+antibodies:+promising+experimental+and+therapeutic+tools+in+infection+and+immunity.">Single domain antibodies: promising experimental and therapeutic tools in infection and immunity.</a> Medical Microbiology and Immunology. 198 (3), 157-174 (2009).</li><li>Harmsen, M. M., De Haard, H. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Properties,+production,+and+applications+of+camelid+single-domain+antibody+fragments.">Properties, production, and applications of camelid single-domain antibody fragments.</a> Applied Microbiology and Biotechnology. 77 (1), 13-22 (2007).</li><li>McMahon, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Yeast+surface+display+platform+for+rapid+discovery+of+conformationally+selective+nanobodies.">Yeast surface display platform for rapid discovery of conformationally selective nanobodies.</a> Nature Structural &amp; Molecular Biology. 25 (3), 289-296 (2018).</li></ol>

Drs. Whiteheart and Hersh are at the University of Kentucky and operate a core in the Center for Molecular Medicine that produces single domain antibodies in alpaca as a fee-for-service.

As noted, the high affinity and specificity of single domain antibodies, combined with their facile expression and stability, make them ideal reagents for the applications in biomedical research, as critical biochemical reagents, diagnostic tools, or therapeutic agents18. For commercial applications, there are some issues related to intellectual property that must be considered. Additionally, single domain antibodies can be engineered to contain specific markers or tags that can be used as reporters in cellular assays or in diagnostics. The key to these uses is the ability to produce specific single domain antibodies against the antigens of interest. A method is described here to produce single domain antibodies using alpacas, which produces a robust immune response against a wide variety of protein antigens. Considerations for animal handling and regulatory compliance are described. These are key for the success in this part of the process.
There are other strategies for producing single domain antibodies that do not require the immunization, but instead use semisynthetic libraries with different systems for the selection and iterative optimization of affinities19,20. However, the advantage of using libraries derived from immunized animals is the ability to reliably isolate highly enriched, diverse, and high-affinity single domain antibodies. Additionally, not only are significant sequence variations observed, but a significant majority of specific single domain antibodies isolated had unique insertions and deletions, particularly in CDR3. 
Further, single domain antibodies can be produced via a straightforward process that only requires small injections of the antigen, and after this process, the animals can be returned to the herd. Of note, the animal can be freely used for fiber production, but must be excluded from use as meat (human food chain) due to the use of the test antigens and non-FDA approved adjuvant for single domain antibody production. When the procedure is completed, the animals should be monitored for one week, given a final veterinary exam, and then can be either returned to their home farm or rested for six months prior to another round of single domain antibody production.

Alpacas, and other members of the camelid family, have become a popular source for generating antibodies for biomedical research1,2,3. Camelids have a unique immune system in that they produce both normal antibodies as well as heavy-chain only antibodies which allow the production of much smaller single domain antibodies, while retaining high specificity and high affinity. Thus, camelid antibodies provide a versatile reagent useful for a variety of purposes. A method to immunize alpaca and produce single domain antibodies to a variety of protein antigens is here described. These antibodies can be produced in camelids via a relatively straightforward process that only requires the immunization via small injections of the target protein (antigen) and a blood draw4. Subsequently, library construction, M13 phage display5 and panning versus the recombinant antigen6 is used to isolate and produce single domain antibodies with the desired characteristics. Because the process takes advantage of the power of phage display technology, five or more antigens can be simultaneously utilized per animal, thereby reducing the number of animals used and associated costs.
Typical mammalian antibodies or immunoglobulins are large molecules consisting of two types of chains (2 heavy chains and 2 light chains), which are linked together through disulfide bonds. These antibodies are relatively large, exhibiting molecular weights of ~140-190 kDa for the more abundant IgG species from humans, mice, goats, and rabbits. Due to their multi-subunit structure, high molecular weight, and disulfide bonds, immunoglobulins can be rather challenging to produce in large quantities, making their cost high. In the 1990&#39;s, it was discovered that camelids, which includes camels, llamas and alpacas make, in addition to the typical mammalian type immunoglobulin, a novel form of immunoglobulin that is simpler in structure, possessing only heavy chains7. These unique camelid antibodies possess the same ability to specifically bind foreign substances with high affinity but are only made up of one protein chain8. Furthermore, camelid antibodies can be experimentally truncated to an even smaller unit the VHH fragment, also called a single domain antibody9. Due to their small size, single domain antibodies are useful for a wide range of biomedical research applications and are available from a variety of academic and commercial sources1,10. An exception appears to be Western blotting since single domain antibodies are more often directed against conformation dependent epitopes, which are usually lost under the denaturing conditions used in Western blots.
Since they are made up of a single polypeptide chain, specific single domain antibodies can be selected and easily produced in large quantities as recombinant proteins in bacteria. Single domain antibodies can also be genetically engineered to contain specific markers or tags that can be used as &#34;reporter groups&#34; for diagnosing diseases11. This ease of manipulation coupled with their flexibility of use makes single domain antibodies an important resource for researchers at universities and elsewhere.
As part of a National Institutes of Health supported core, existing methods have been adapted to produce single domain antibodies from alpacas3,4. Alpacas have significant advantages in both ease of handling relative to larger camelid family members as well as accessibility. Alpacas are widely raised for fiber and meat and thus can be obtained regionally from local alpaca farmers, who can be identified through their websites or through state breeder associations. Two breeds of alpacas are available, Suri and Huacaya. Huacaya are more common and were used for this protocol, but the protocol is generally applicable to either breeds and also more widely applicable to other camelids.

<table border="0" cellpadding="0" cellspacing="0" style="width:932px;" width="932">
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:299px;">GERBU FAMA adjuvant</td>
			<td style="width:123px;">Biotechnik, Heidelberg, Germany&#160;</td>
			<td style="width:344px;">3003,6001</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Serum collection tube</td>
			<td>Becton Dickinson</td>
			<td>367983</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Blood collection tube</td>
			<td>Becton Dickinson</td>
			<td>366643</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Vacutainer blood collection set</td>
			<td>Becton Dickinson</td>
			<td>368652</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Maxisorp Immuno plates</td>
			<td>Nunc</td>
			<td>439454</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">BSA</td>
			<td>Sigma-Aldrich</td>
			<td>A7906</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">HRP-conjugated goat anti-llama IgG antibody&#160;</td>
			<td>Bethyl Labs</td>
			<td>A160-100P</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">TMB reagent chromogenic peroxidase substrate&#160;</td>
			<td>KPL</td>
			<td>50-76-03</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Plate Reader</td>
			<td>Spectramax</td>
			<td>M5</td>
			<td>Any UV/VIS capable reader is acceptable</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Uni-SepMAXI+ lyphocyte separation tube</td>
			<td>Novamed</td>
			<td>U-17</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">RNeasy Mini Kit</td>
			<td>Qiagen</td>
			<td>74104</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">QIAshredder column</td>
			<td>Qiagen</td>
			<td>79654</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Superscript IV reverse transcriptase&#160;&#160;</td>
			<td>Invitrogen</td>
			<td>18064014</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">AEBSF solution</td>
			<td>Biosynth</td>
			<td>A-5440</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">TG1 phage display competent cells</td>
			<td>Lucigen</td>
			<td>60502</td>
			<td></td>
		</tr>
	</tbody>
</table>

immunization of alpacas (lama pacos) with protein antigens and production of antigen-specific single domain antibodies

In this manuscript, a method for the immunization of alpaca and the use of molecular biology methods to produce antigen-specific single domain antibodies is described and demonstrated. Camelids, such as alpacas and llamas, have become a valuable resource for biomedical research since they produce a novel type of heavy chain-only antibody which can be used to produce single domain antibodies. Because the immune system is highly flexible, single domain antibodies can be made to many different protein antigens, and even different conformations of the antigen, with a very high degree of specificity. These features, among others, make single domain antibodies an invaluable tool for biomedical research. A method for the production of single domain antibodies from alpacas is reported. A protocol for immunization, blood collection, and B-cell isolation is described. The B-cells are used for the construction of an immunized library, which is used in the selection of specific single domain antibodies via panning. Putative specific single domain antibodies obtained via panning are confirmed by pull-down, ELISA, or gel-shift assays. The resulting single domain antibodies can then be used either directly or as a part of an engineered reagent. The uses of single domain antibody and single domain antibody-based regents include structural, biochemical, cellular, in vivo, and therapeutic applications. Single domain antibodies can be produced in large quantities as recombinant proteins in prokaryotic expression systems, purified, and used directly or can be engineered to contain specific markers or tags that can be used as reporters in cellular studies or in diagnostics.

The protocol presented here was utilized to generate single domain antibodies against a range of protein antigens. Five antigens were utilized per alpaca. Immune monitoring indicated that the majority of antigens showed robust response beginning at three weeks (Figure 1). Production bleeds and library construction after approximately six weeks gives the best balance for the animals that have multiple antigens injected. Two rounds of panning were performed for each antigen, and isolated colonies screened (Figure 2). Sequencing of positive colonies identified diverse single domain antibody sequences for the different antigens. For examples, three unique clones were isolated to the reference antigen Maltose Binding Protein (MBP) (Figure 3A). As is frequently observed, the single domain antibodies contain significant sequence diversity and highly variable CDR3 length (Figure 3). These features are particularly important in single domain antibody/antigen interactions as seen in the reference single domain antibody/CX3CL1 complex17 (Figure 3B).
The majority of full-length single domain antibody sequences can be expressed and purified at 1-10 mg/L of culture (Figure 4A). Because of the diversity in CDR3 length, different single domain antibodies show slight variation in molecular weight. Confirmation of direct binding and application specific performance is critical. For example, after two rounds of selection against Antigen B, a panel of single domain antibodies were identified (Figure 2). Multiple identical sequences were identified, and the single domain antibody was produced and purified. It was then tested via direct pull down with antigen affinity resin and showed robust dose-dependent binding (Figure 4B). Importantly, the single domain antibody showed no binding to control resin. These data demonstrate a direct binding interaction, and one that is well suited for affinity capture in both pull-down and ELISA-based formats.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/58471/58471fig1.jpg" /> 
Figure 1: Representative immune monitoring of two distinct antigens showing the significant specific immune response to distinct antigens in the same animal. Many antigens show robust response as early as three weeks after commencing immunization, with the majority showing maximal response after six weeks. Six weeks also allows for affinity maturation and is the recommended time for the production bleed and B-cell isolation. <a href="https://www.jove.com/files/ftp_upload/58471/58471fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/58471/58471fig2.jpg" /> 
Figure 2: PCR-based confirmation of positive clones. Primers span the MCS of the pMES4 vector, and a positive nanobody clone produces an amplicon of ~500 bp (marked with *). <a href="https://www.jove.com/files/ftp_upload/58471/58471fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/58471/58471fig3.jpg" /> 
Figure 3: Antigen-specific sequences highlight alpaca single domain antibody diversity. (A) Alignment of select single domain antibody sequences isolated to MBP with a reference single domain antibody 4XT1, with framework and complementarity-determining regions (Kabat) highlighted below. (B) Structure of alpaca single domain antibody 4XT1 bound to CX3CL1 (PDB 4XT1), emphasizing the critical role of variable CDR loops in specific antigen binding. <a href="https://www.jove.com/files/ftp_upload/58471/58471fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/58471/58471fig4.jpg" /> 
Figure 4: Purification and validation of single domain antibodies. (A) SDS-PAGE of IMAC purified single domain antibodies, comparing diverse single domain antibodies. Different molecular weights are primarily due to varying length of the CDR3 loop. Differing levels of expression are also observed, with a minority of single domain antibodies showing poor yields of purified protein. (B) Verification of direct binding using an antigen affinity pull-down. Robust dose-dependent single domain antibody binding is observed with antigen-coupled resin but not with control resin.&#160;<a href="https://www.jove.com/files/ftp_upload/58471/58471fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Immunization of Alpacas Lama pacos with Protein Antigens and Production of Antigen-specific Single Domain Antibodies at JoVE.com

Immunization of Alpacas Lama pacos with Protein Antigens and Production of Antigen-specific Single Domain Antibodies

A method for the production of single domain antibodies from alpacas, including immunization, blood collection, B-cell isolation, and selection is described.

Immunization of Alpacas (Lama pacos) with Protein Antigens and Production of Antigen-specific Single Domain Antibodies

In this manuscript, a method for the immunization of alpaca and the use of molecular biology methods to produce antigen-specific single domain antibodies ...

immunization-alpacas-lama-pacos-with-protein-antigens-production

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23.3K Views.  University of Kentucky. A method for the production of single domain antibodies from alpacas, including immunization, blood collection, B-cell isolation, and selection is described.

Video: Immunization of Alpacas Lama pacos with Protein Antigens and Production of Antigen-specific Single Domain Antibodies

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique applications for OMV where traditional nanoparticles are proving too difficult to synthesize. To date, all Gram-negative bacteria have been shown to produce OMV demonstrating packaging of a variety of cargo that includes small molecules, peptides, proteins and genetic material. Based on their diverse cargo, OMV are implicated in many biological processes ranging from cell-cell communication to gene transfer and delivery of virulence factors depending upon which bacteria are producing the OMV. Only recently have bacterial OMV become accessible for use across a wide range of applications through the development of techniques to control and direct packaging of recombinant proteins into OMV. This protocol describes a method for the production, purification, and use of enzyme packaged OMV providing for improved overall production of recombinant enzyme, increased vesiculation, and enhanced enzyme stability. Successful utilization of this protocol will result in the creation of a bacterial strain that simultaneously produces a recombinant protein and directs it for OMV encapsulation through creating a synthetic linkage between the recombinant protein and an outer membrane anchor protein. This protocol also details methods for isolating OMV from bacterial cultures as well as proper handling techniques and things to consider when adapting this protocol for use for other unique applications such as: pharmaceutical drug delivery, medical diagnostics, and environmental remediation.

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

A protocol for the production, purification, and use of enzyme packaged outer membrane vesicles (OMV) providing for enhanced enzyme stability for implementation across diverse applications is presented.

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique ...

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. Atomic force microscopy (AFM) can address this problem by enabling stretching and relaxation of single protein molecules, which gives direct evidence of specific unfolding and refolding characteristics. AFM-based single-molecule force-spectroscopy (AFM-SMFS) provides a means to consistently measure high-energy conformations in proteins that are not possible in traditional bulk (biochemical) measurements. Although numerous papers were published to show principles of AFM-SMFS, it is not easy to conduct SMFS experiments due to a lack of an exhaustively complete protocol. In this study, we briefly illustrate the principles of AFM and extensively detail the protocols, procedures, and data analysis as a guideline to achieve good results from SMFS experiments. We demonstrate representative SMFS results of single protein mechanical unfolding measurements and we provide troubleshooting strategies for some commonly encountered problems.

We describe the detailed procedures and strategies to measure the mechanical properties and mechanical unfolding pathways of single protein molecules using an atomic force microscope. We also show representative results as a reference for selection and justification of good single protein molecule recordings.

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. ...

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.

A procedure is presented for the refolding of the dCACHE periplasmic ligand binding domain of Campylobacter jejuni chemoreceptor Tlp3 from inclusion bodies and the purification to yield milligram quantities of protein.

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be ...

Covalent Immobilization of Proteins for the Single Molecule Force Spectroscopy

In recent years, atomic force microscopy (AFM) based single molecule force spectroscopy (SMFS) extended our understanding of molecular properties and functions. It gave us the opportunity to explore a multiplicity of biophysical mechanisms, e.g., how bacterial adhesins bind to host surface receptors in more detail. Among other factors, the success of SMFS experiments depends on the functional and native immobilization of the biomolecules of interest on solid surfaces and AFM tips. Here, we describe a straightforward protocol for the covalent coupling of proteins to silicon surfaces using silane-PEG-carboxyls and the well-established N-hydroxysuccinimid/1-ethyl-3-(3-dimethyl-aminopropyl)carbodiimid (EDC/NHS) chemistry in order to explore the interaction of pilus-1 adhesin RrgA from the Gram-positive bacterium Streptococcus pneumoniae (S. pneumoniae) with the extracellular matrix protein fibronectin (Fn). Our results show that the surface functionalization leads to a homogenous distribution of Fn on the glass surface and to an appropriate concentration of RrgA on the AFM cantilever tip, apparent by the target value of up to 20% of interaction events during SMFS measurements and revealed that RrgA binds to Fn with a mean force of 52 pN. The protocol can be adjusted to couple via site specific free thiol groups. This results in a predefined protein or molecule orientation and is suitable for other biophysical applications besides the SMFS.

This protocol describes the covalent immobilization of proteins with a heterobifunctional silane coupling agent to silicon-oxide surfaces designed for the atomic force microscopy based single molecule force spectroscopy which is exemplified by the interaction of RrgA (pilus-1 tip adhesin of S. pneumoniae) with fibronectin.

In recent years, atomic force microscopy (AFM) based single molecule force spectroscopy (SMFS) extended our understanding of molecular properties and ...

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing approaches suffer from significant limitations, we have developed a new method for determining TF-DNA binding affinities with high sensitivity on a large scale. The assay relies on the established fluorescence anisotropy (FA) principle but introduces important technical improvements. First, we measure a full FA competitive titration curve in a single well by incorporating TF and a fluorescently labeled reference DNA in a porous agarose gel matrix. Unlabeled DNA oligomer is loaded on the top as a competitor and, through diffusion, forms a spatio-temporal gradient. The resulting FA gradient is then read out using a customized epifluorescence microscope setup. This improved setup greatly increases the sensitivity of FA signal detection, allowing both weak and strong binding to be reliably quantified, even for molecules of similar molecular weights. In this fashion, we can measure one titration curve per well of a multi-well plate, and through a fitting procedure, we can extract both the absolute dissociation constant (KD) and active protein concentration. By testing all single-point mutation variants of a given consensus binding sequence, we can survey the entire binding specificity landscape of a TF, typically on a single plate. The resulting position weight matrices (PWMs) outperform those derived from other methods in predicting in vivo TF occupancy. Here, we present a detailed guide for implementing HiP-FA on a conventional automated fluorescent microscope and the data analysis pipeline.

Here we present a novel method for determining binding affinities at equilibrium and in solution with high sensitivity on a large scale. This improves the quantitative analysis of transcription factor-DNA binding. The method is based on automated fluorescence anisotropy measurements in a controlled delivery system.

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

NEMO is a scaffolding protein which plays an essential role in the NF-&#954;B pathway by assembling the IKK-complex with the kinases IKK&#945; and IKK&#946;. Upon activation, the IKK complex phosphorylates the I&#954;B molecules leading to NF-&#954;B nuclear translocation and activation of target genes. Inhibition of the NEMO/IKK interaction is an attractive therapeutic paradigm for the modulation of NF-&#954;B pathway activity, making NEMO a target for inhibitors design and discovery. To facilitate the process of discovery and optimization of NEMO inhibitors, we engineered an improved construct of the IKK-binding domain of NEMO that would allow for structure determination of the protein in the apo form and while bound to small molecular weight inhibitors. Here, we present the strategy utilized for the design, expression and structural characterization of the IKK-binding domain of NEMO. The protein is expressed in E. coli cells, solubilized under denaturing conditions and purified through three chromatographic steps. We discuss the protocols for obtaining crystals for structure determination and describe data acquisition and analysis strategies. The protocols will find wide applicability to the structure determination of complexes of NEMO and small molecule inhibitors.

We describe protocols for the structure determination of the IKK-binding domain of NEMO by X-ray crystallography. The methods include protein expression, purification and characterization as well as strategies for successful crystal optimization and structure determination of the protein in its unbound form.

NEMO is a scaffolding protein which plays an essential role in the NF-&#954;B pathway by assembling the IKK-complex with the kinases IKK&#945; and ...

Production of Dynein and Kinesin Motor Ensembles on DNA Origami Nanostructures for Single Molecule Observation

Cytoskeletal motors are responsible for a wide variety of functions in eukaryotic cells, including mitosis, cargo transport, cellular motility, and others. Many of these functions require motors to operate in ensembles. Despite a wealth of knowledge about the mechanisms of individual cytoskeletal motors, comparatively less is known about the mechanisms and emergent behaviors of motor ensembles, examples of which include changes to ensemble processivity and velocity with changing motor number, location, and configuration. Structural DNA nanotechnology, and the specific technique of DNA origami, enables the molecular construction of well-defined architectures of motor ensembles. The shape of cargo structures as well as the type, number and placement of motors on the structure can all be controlled. Here, we provide detailed protocols for producing these ensembles and observing them using total internal reflection fluorescence microscopy. Although these techniques have been specifically applied for cytoskeletal motors, the methods are generalizable to other proteins that assemble in complexes to accomplish their tasks. Overall, the DNA origami method for creating well-defined ensembles of motor proteins provides a powerful tool for dissecting the mechanisms that lead to emergent motile behavior.

The goal of this protocol is to form ensembles of molecular motors on DNA origami nanostructures and observe the ensemble motility using total internal reflection fluorescence microscopy.

Cytoskeletal motors are responsible for a wide variety of functions in eukaryotic cells, including mitosis, cargo transport, cellular motility, and ...

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the dissection and manipulation of biological pathways. Currently, only a limited number of chemically induced dimerization (CID) systems exist and engineering new ones with desired sensitivity and selectivity for specific small-molecule ligands remains a challenge in the field of protein engineering. We here describe a high throughput screening method, combinatorial binders-enabled selection of CID (COMBINES-CID), for the de novo engineering of CID systems applicable to a large variety of ligands. This method uses the two-step selection of a phage-displayed combinatorial nanobody library to obtain 1) &#34;anchor binders&#34; that first bind to a ligand of interest and then 2) &#34;dimerization binders&#34; that only bind to anchor binder-ligand complexes. To select anchor binders, a combinatorial library of over 109 complementarity-determining region (CDR)-randomized nanobodies is screened with a biotinylated ligand and hits are validated with the unlabeled ligand by bio-layer interferometry (BLI). To obtain dimerization binders, the nanobody library is screened with anchor binder-ligand complexes as targets for positive screening and the unbound anchor binders for negative screening. COMBINES-CID is broadly applicable to select CID binders with other immunoglobulin, non-immunoglobulin, or computationally designed scaffolds to create biosensors for in vitro and in vivo detection of drugs, metabolites, signaling molecules, etc.

Creating chemically induced protein dimerization systems with desired affinity and specificity for any given small molecule ligand would have many biological sensing and actuation applications. Here, we describe an efficient, generalizable method for de novo engineering of chemically induced dimerization systems via the stepwise selection of a phage-displayed combinatorial single-domain antibody library.

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the ...

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy

Chemical and bio-conjugation techniques have been developed rapidly in recent years and allow the building of protein polymers. However, a controlled protein polymerization process is always a challenge. Here, we have developed an enzymatic methodology for constructing polymerized protein step by step in a rationally-controlled sequence. In this method, the C-terminus of a protein monomer is NGL for protein conjugation using OaAEP1 (Oldenlandia affinis asparaginyl endopeptidases) 1) while the N-terminus was a cleavable TEV (tobacco etch virus) cleavage site plus an L (ENLYFQ/GL) for temporary N-terminal protecting. Consequently, OaAEP1 was able to add only one protein monomer at a time, and then the TEV protease cleaved the N-terminus between Q and G to expose the NH2-Gly-Leu. Then the unit is ready for next OaAEP1 ligation. The engineered polyprotein is examined by unfolding individual protein domain using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Therefore, this study provides a useful strategy for polyprotein engineering and immobilization.

Here, we present a protocol to conjugate protein monomer by enzymes forming protein polymer with a controlled sequence and immobilize it on the surface for single-molecule force spectroscopy studies.

Chemical and bio-conjugation techniques have been developed rapidly in recent years and allow the building of protein polymers. However, a controlled ...